Abstract More than 12 million people in the United States are living with HIV infection. The increased life expectancy of the HIV-positive population associated with the development of neurological complications. Morbidity and life expectancy of HIV-positive individuals are significantly affected by drugs of abuse. In developed countries, approximately 30% of HIV-positive individuals are intravenous drug abusers, and the risk of HAND increased among those individuals. The major drugs contributing to HIV pathogenesis are opiates (morphine) and stimulants (cocaine and methamphetamine). Cocaine is the second most commonly abused drug in the US and cocaine abuse in HIV-infected patients is associated with worsening of HAND. Thus, investigation of mechanisms of synergetic neurotoxicity of HIV proteins and drugs of abuse is a valuable avenue for development of HAND therapy. Our long term goal is to determine new targets for the development of HAND therapy. The present application is re-submitted in response to PA-15-290 ?AIDS-Science Track Award for Research Transition (R03).? In this application, our objective is to apply functional genomics approaches to understand the molecular mechanism of synergistic neurotoxicity of HIV Tat protein and cocaine. The proposed approach is the transition of functional screenings technologies we developed and successfully applied for discovery of new targets for anti-cancer therapy (Shtutman et al., 2011, Levina et al., 2015) to the discovery of new molecular mechanisms cognitive impairment associated with combined effects of HIV and drugs of abuse. The approach will be applied to functional profiling of the pathways regulated combined neurotoxicity of Tat and cocaine. To fulfill our goal we propose two specific aims: 1) Determine critical pathways are impacting Tat-induced neurotoxicity in mouse cortical neurons and 2) Determine genes and pathways which are predominant for Tat toxicity and the synergistic toxicity by TAT and cocaine on cultures of human neurons The approach is significant because it provides comprehensive information about genes and pathways regulated synergetic neurotoxicity of HIV and drugs of abuse in primary neurons. This approach is innovative since the proposed research adopts new NGS based functional screening technologies and statistical analyses that we have developed to determine genes and pathways involved in the synergetic toxicity of HIV and drugs of abuse of a test case of combined effects of Tat and cocaine. This study is anticipated to set a standard model approach for understanding how HIV and drugs of abuse promote neuronal damage and death, including both direct and indirect effects of HIV proteins in combinations with opiates and stimulants. Furthermore, these approaches can then be applied to a variety of systems from primary neuronal culture to animal models of HAND, to further explore novel therapeutic targets for treatment of HAND